Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgttgcttctgtccattgttgtgtttgatcattgaaaacccacaatttgcatggtttatctcaccgtaaaaatgattttcttttcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA

Basic information

species Vitis vinifera
transcript Vv13s0019g03470.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g01450.1 (Oryza sativa), 3'ss of exon 5
tctgttgcttctgtccattgttgtgtttgatcattgaaaacccacaatttgcatggtttatctcaccgtaaaaatgattttcttttcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA
  |  |||||  |    | | | ||   | | | |||| | |    |||| ||   ||| |   ||    | ||| |||      |   ||  |  | ||||  |  |    ||  ||||| ||||||||||||||||||||||| | ||| |||| || ||||||||||| || || ||||||| ||||     ||  |
gttagtgctttagcttgtcggtatgcgag-taaatgaatatc----attttca-attttcttgtac----ataatcattgcaccatttggtgat--gcagGATAATCTTGCACTGGTGTACCTGTCAAGCATCACAAGGACACAGATTAGCATAGCCGAGAAGTTGAACACCGCCGCCCAAATCCTGTAATTTCCATGTA

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G025214_T03 (Zea mays), 3'ss of exon 10
----tctgttgc----ttctgtccattgttgtgtttgatcattgaaaacccacaatttgcatggtttatctcaccgtaaaaatgattttcttttcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA
    ||  |  |    ||| |   | |    |||     | ||   |  |||   | || |||||  | ||  | |   |  | |||     |  |||        ||||  || |    ||  | ||| ||||||||||||||||||||||  | ||| | || || ||||||||||| ||||||||| | | |||           
cttttcaatgacaagattcaggtaaattacttgtgcaccccttttgatgcca--gtgtggatggta-accttgctgatgatctaattaataatcactgacccc-

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G025214_T01 (Zea mays), 3'ss of exon 9
tctgttgcttctgtccattgttgtgtttgatcattgaaaacccacaatttgcatggtttatctcaccgtaaaaatgattttcttttcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA-
            ||  |||  | |||     | ||   |  |||   | || |||||  | ||  | |   |  | |||     |  |||        ||||  || |    ||  | ||| ||||||||||||||||||||||  | ||| | || || ||||||||||| ||||||||| | | |||     |  |   
------------gtaaattact-tgtgcaccccttttgatgcca--gtgtggatggta-accttgctgatgatctaattaataatcactgacccc-acagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGCATCGCCGAGAAGTTGAACACTGCTGCTCAAGTGCTGTAGGTT-TGGCGGT

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G098153_T03 (Zea mays), 3'ss of exon 1
tctgttgcttctgtccattgttgtgtttgatcat--tgaaaacccacaatttgcatggtttatctcaccgtaaaaatgattttcttttcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA
            ||  ||| || | || | || |  ||  |    |  ||   ||  ||   | |    |   |   ||||  |  |  | |        ||||  || |    ||  | ||| ||||||||||||||||||||||  | ||| | || || ||||||||||| ||||||||    | || ||     |   
------------gtaaattatttttttggctcttgatggcagtgtaggatagccaccgtgctttttcttgctgatg-gattaacaataaccgacccc-acagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGCATCGCCGAGAAGTTGAACACTGCTGCTCAGGCGCTGTGACTTTGGTTGT

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G42210.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------tctgttgcttctgtccattgttgtgtttgatcattgaaaacccacaatttgcatggtttatctcaccgtaaaaatgattttcttttcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA
                                                        || |||   | |||   |  |    ||||||||   |     ||||  ||  | | |||   |   | || ||  |  ||||| || |    |||   |||||||||| ||| | || || || ||||||||||| ||||||||||| ||| | || ||||||||||| || |||||||| ||   || |          
gtaagattaagttttgatcatgttttatggccactaaataaaatctatcttttgagtcagtttgctatgttgttgataagttttgatcaagtattcaacacatcttctaagtttttgtttggcttacaagagtgtttctgtttcatcctttc--agGACCACTTGCTCTTGCTATATTTATCAAGCATCACTAGGACACAGCTTAGCCTGGCAGAAAAGTTGAATACGGCTGCTCAGATTTTGTGA----------

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G06690.1 (Glycine max), 3'ss of exon 5
------------------------------------------tctgttgcttctgtccattgttgtgtttgatcattgaaaacccacaatttgcatggtttatctcaccgtaaaaatgattttcttt--tcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA-
                                          ||| |||  || ||     | |||  ||||| | |    | | |  ||        | |         ||    ||  || |     |  |  |  ||| |||||||||| ||| | || || || ||||||||||| ||||||||||| ||| | || ||||||||||| || |||||||| ||   || |  | | || | 
gtaagataaagttttgatcatgttttcactatataaaatctatcttttgaatcagtttgc-gatgttgttgataagttttgatcaagtatccaacacatcttctcagttttatttttggcttacaagagtgttaatccttgcagGACCACTTGCTCTTGCTATATTTATCAAGCATCACTAGGACACAGCTTAGCCTGGCAGAAAAGTTGAATACGGCTGCTCAGATTTTGTGATTC-TGTCTAT

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G03340.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------------tctgttgcttctgtccattgttgtgtttgatcattgaaaacccacaatttgcatggtttatctcaccgtaaaaatgattttcttttcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA
                                                                                 | ||| ||||     || ||| | |||       |     | ||  ||||   ||  ||       |     |||      | |    |   ||  |||| ||||| ||  | ||||| || || || |||||||| || ||||| ||||| || ||||| ||||||||||||||||| || | || |  | |   | 
ggtaagattatgctttgtgttagtggtttattactgggatttcttattttgatgaaaattgtgaaatgagatggaacagatttttgtttcttatatttattg-gcttgtcaggcaagtcttctcagcttgcc--gtccatagttttattgtgctgacaggggtgtttcatccatttcaGGATCACTTGCTTTTGCTGTATTTATCTAGTATCACAAGAACGCAGCTTAGCTTGGCTGAAAAATTGAACACAGCTGCTCAGATTCTGTGATTCTTCCGC-

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G39990.1 (Arabidopsis thaliana), 3'ss of exon 5
tctgttgcttctgtccattgttgtgtttgatcattgaaaacccacaatttgcatggtttatctcaccgtaaa--aatgattttcttttcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA
                          |  |  |||| |||     |             |  |      |||  |||| || | | ||| |||| |||  ||||||| || || ||  ||||| | |||||||| |||||||||||| ||||  ||||||| ||| | ||||||||||||||||| |  |||      |  |
-------------------------gtaaaagattgtaaatttcaagccaaagcaaaacactttgtaaaaaactaatggttgtttcttc-tgttattt-cagGACCAATTGCTTCTGTTGTACCTATCAAGCATAACAAGGACACAGTTGAGTCTAGCGGAGAAGCTAAACACAGCTGCTCAAATGCTATAATAAGCTTGGA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110380965|gb|EC946269.1|EC946269
EST:     CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAG                         GACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
genomic: CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAGgtaagacaat ... ttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
EST: gi|32268757|gb|CD717916.1|CD717916
EST:     CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAG                         GACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
genomic: CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAGgtaagacaat ... ttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
EST: gi|71884916|gb|DT033971.1|DT033971
EST:     CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAG                         GACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
genomic: CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAGgtaagacaat ... ttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
EST: gi|110401608|gb|EC968223.1|EC968223
EST:     CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAG                         GACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
genomic: CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAGgtaagacaat ... ttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
EST: gi|110361955|gb|EC925461.1|EC925461
EST:     CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAG                         GACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
genomic: CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAGgtaagacaat ... ttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
EST: gi|71886521|gb|DT035576.1|DT035576
EST:     CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAG                         GACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
genomic: CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAGgtaagacaat ... ttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
EST: gi|30128322|gb|CB913661.1|CB913661
EST:     CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAG                         GACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
genomic: CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAGgtaagacaat ... ttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
EST: gi|110387531|gb|EC952206.1|EC952206
EST:     CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAG                         GACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGACC
genomic: CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAGgtaagacaat ... ttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
EST: gi|110375382|gb|EC940363.1|EC940363
EST:     CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAG                         GACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
genomic: CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAGgtaagacaat ... ttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
EST: gi|30134061|gb|CB919399.1|CB919399
EST:     CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAG                         GACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC
genomic: CCAAAATTTCACCTCCAGCTTTTGATAGGCTGGTGAATGACAGCCTTCAGgtaagacaat ... ttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgcatggtttatctcaccgtaaaaatgattttcttttcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA
              atctcac  putative branch site (score: 3)
                                ttttcttttcctgttt  putative PPT
                       taaaaatgattttctt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgttgcttctgtccattgttgtgtttgatcattgaaaacccacaatttgcatggtttatctcaccgtaaaaatgattttcttttcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- tgttgct
- - - - - ctgtcca
- - - - - - - - - tgttgtg
- - - - - - - - - - - - - - - - - - -aaaccca
- - - - - - - - - - - - - - - - - - - - - - - - - gcatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaaa